Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle

Abstract

The Toll-like receptor (TLR) and peptidoglycan recognition protein 1 (PGLYRP1) genes play key roles in the innate immune systems of mammals. While the TLRs recognize a variety of invading pathogens and induce innate immune responses, PGLYRP1 is directly microbicidal. We used custom allele-specific assays to genotype and validate 220 diallelic variants, including 54 nonsynonymous SNPs in 11 bovine innate immune genes (TLR1-TLR10, PGLYRP1) for 37 cattle breeds. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and we were unable to differentiate between the specialized B. t. taurus beef and dairy breeds, despite an average polymorphism density of one locus per 219 bp. Ninety-nine tagSNPs and one tag insertion-deletion polymorphism were sufficient to predict 100% of the variation at all 11 innate immune loci in both subspecies and their hybrids, whereas 58 tagSNPs captured 100% of the variation at 172 loci in B. t. taurus. PolyPhen and SIFT analyses of nonsynonymous SNPs encoding amino acid replacements indicated that the majority of these substitutions were benign, but up to 31% were expected to potentially impact protein function. Several diversitybased tests provided support for strong purifying selection acting on TLR10 in B. t. taurus cattle. These results will broadly impact efforts related to bovine translational genomics.peptidoglycan recognition protein | bovine translational genomics | bovine Toll-like receptors | single nucleotide polymorphism

Determination of Genetic Variations of Toll-like Receptor (TLR) 2, 4 and 6 with Next Generation Sequencing in Native Cattle Breeds of Anatolia and Holstein Friesian

“…In comparison with previous studies [34,46,47] highest variation number found in the analyzed genes in Anatolian breeds except for TLR4, where HOL breed has more variations than AB and TG breeds. In these studies, researchers sampled minimum one individual of each breed that went under artificial selection and analyzed innate immunity related genes partially.…”

Genomic response to natural selection within alpine cattle breeds

“…One of the tools suggested to improve inherited animal health is breeding for enhanced immune response. The mammalian innate immune system provides host defence against a variety of pathogens without requiring prior exposure, and genes modulating innate immunity have often been considered candidate loci for improving the host resistance to disease (Seabury et al 2009). The immune system is regulated by several thousand genes (8-9% of the genome) that indicate its high genetic priority as a critical fitness trait providing survival of the species (Mallard et al 2015).…”

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

“…As noted earlier, the IBHM included a wide group of breeds, including B. taurus, B. indicus, and hybrid breeds. Given their diverse domestication history and documented genomic differences (e.g., Brunelle et al 2008;Bovine HapMap Consortium et al 2009;Seabury et al 2010), including both taurine and indicine breeds in the study had the potential to introduce ascertainment bias. A parallel study was thus done to examine this possibility.…”

“…However, several features of the analysis applied herein were assumed to render it relatively robust against ascertainment bias. First, the basis for the study was a large group of very diverse breeds (Brunelle et al 2008;Bovine HapMap Consortium et al 2009;Seabury et al 2010), For each chromosome (BTA), the length in base pairs (Mbp), the number of evaluated genotypes (SNP), SNP density statistics, and the critical values of the negative composite log likelihood (CCLL) above which significance was declared as P , 0.01 on a genome-wide level for single-and 5-breed subpopulations.…”